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- PDB-5lsr: Carboxysome shell protein CcmP from Synechococcus elongatus PCC 7942 -

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Basic information

Entry
Database: PDB / ID: 5lsr
TitleCarboxysome shell protein CcmP from Synechococcus elongatus PCC 7942
ComponentsCcmP
KeywordsTRANSPORT PROTEIN / Carboxysome Shell protein BMC domain Gated transport
Function / homology
Function and homology information


structural constituent of carboxysome shell / carboxysome / carbon fixation / photosynthesis
Similarity search - Function
Bacterial microcompartment (BMC) circularly permuted domain / Bacterial microcompartment (BMC) circularly permuted domain profile. / BMC (bacterial microcompartment) domain / Bacterial microcompartment domain / BMC / CcmK-like superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
THIOCYANATE ION / Carboxysome shell protein CcmP
Similarity search - Component
Biological speciesSynechococcus elongatus PCC 7942 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsLarsson, A.M. / Hasse, D. / Valegard, K. / Andersson, I.
Funding support Sweden, 4items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Knut and Alice Wallenberg Foundation Sweden
European Research Council Sweden
Rontgen-Angstrom Cluster Sweden
CitationJournal: J. Exp. Bot. / Year: 2017
Title: Crystal structures of beta-carboxysome shell protein CcmP: ligand binding correlates with the closed or open central pore.
Authors: Larsson, A.M. / Hasse, D. / Valegard, K. / Andersson, I.
History
DepositionSep 5, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CcmP
B: CcmP
C: CcmP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9315
Polymers72,8153
Non-polymers1162
Water6,431357
1
A: CcmP
B: CcmP
C: CcmP
hetero molecules

A: CcmP
B: CcmP
C: CcmP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,86210
Polymers145,6306
Non-polymers2324
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_555-x+1/2,y,-z1
Buried area20630 Å2
ΔGint-76 kcal/mol
Surface area39220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.740, 178.740, 178.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-461-

HOH

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Components

#1: Protein CcmP


Mass: 24271.646 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus PCC 7942 (bacteria)
Gene: Synpcc7942_0520 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI / References: UniProt: Q31QW7
#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20 mM BIS-tris propane, 50 mM NaCl, 0.1 mM RuBP, 0.1 mM TrisHCl pH 7, 0.2 mM potassium thiocyanate, 6% poly-alpha-glutamic acid,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.65→44.69 Å / Num. obs: 113271 / % possible obs: 100 % / Redundancy: 20.1 % / Biso Wilson estimate: 29.15 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Net I/σ(I): 18.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.65-1.6817.61.4042.30.7641100
9.04-44.6919.70.07148.30.998199.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.1.29data scaling
BUSTER-TNT1.10.0refinement
PDB_EXTRACT3.2data extraction
XDSNovember 3, 2014data reduction
PHASER2.5.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HT5

4ht5


Resolution: 1.65→44.68 Å / Cor.coef. Fo:Fc: 0.9583 / Cor.coef. Fo:Fc free: 0.9578 / SU R Cruickshank DPI: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.07 / SU Rfree Blow DPI: 0.067 / SU Rfree Cruickshank DPI: 0.067
RfactorNum. reflection% reflectionSelection details
Rfree0.1911 5675 5.01 %RANDOM
Rwork0.1813 ---
obs0.1818 113268 100 %-
Displacement parametersBiso max: 116.31 Å2 / Biso mean: 32.66 Å2 / Biso min: 17.72 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.205 Å
Refinement stepCycle: final / Resolution: 1.65→44.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4714 0 6 357 5077
Biso mean--37.15 39.89 -
Num. residues----616
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1742SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes127HARMONIC2
X-RAY DIFFRACTIONt_gen_planes725HARMONIC5
X-RAY DIFFRACTIONt_it4849HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion638SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5931SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4849HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6570HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion3.79
X-RAY DIFFRACTIONt_other_torsion15.06
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2105 410 4.91 %
Rwork0.2028 7940 -
all0.2032 8350 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5079-0.21920.38780.4756-0.27460.9610.013-0.0852-0.06490.01520.03660.0791-0.073-0.1518-0.0495-0.02410.0214-0.028-0.00790.0178-0.002726.2932-50.99420.9587
20.85140.19760.48320.50220.27390.996-0.1288-0.11650.16610.0025-0.00450.0755-0.4035-0.18720.13330.120.1075-0.0798-0.1238-0.0288-0.045727.2205-17.90142.3463
30.4803-0.04520.14330.91770.03370.6764-0.0497-0.15140.05410.07910.03230.0496-0.2237-0.08060.01740.02010.0336-0.0328-0.0229-0.017-0.050844.1237-35.878224.4128
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 207
2X-RAY DIFFRACTION2{ B|* }B2 - 207
3X-RAY DIFFRACTION3{ C|* }C3 - 207

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